OpenRaiser/Intern-Atlas huggingface dataset:
Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
Venue: arXiv cs.CE 2024
Year: 2024

Predicting the change in binding free energy ($ΔΔG$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $ΔΔG$ data, existing methods focus on pre-training, while neglecting the importance of alignment. In this work, we propose the Boltzmann Alignment technique to transfer knowledge from pre-trained inverse folding models to $ΔΔG$ prediction. We begin by analyzing the thermodynamic definition of $ΔΔG$ and introducing the Boltzmann distribution to connect energy with protein conformational distribution. However, the protein conformational distribution is intractable; therefore, we employ Bayes' theorem to circumvent direct estimation and instead utilize the log-likelihood provided by protein inverse folding models for $ΔΔG$ estimation. Compared to previous inverse folding-based methods, our method explicitly accounts for the unbound state of protein complex in the $ΔΔG$ thermodynamic cycle, introducing a physical inductive bias and achieving both supervised and unsupervised state-of-the-art (SoTA) performance. Experimental results on SKEMPI v2 indicate that our method achieves Spearman coefficients of 0.3201 (unsupervised) and 0.5134 (supervised), significantly surpassing the previously reported SoTA values of 0.2632 and 0.4324, respectively. Futhermore, we demonstrate the capability of our method on binding energy prediction, protein-protein docking and antibody optimization tasks.
The Future of Learning in the Age of Generative AI: Automated Question Generation and Assessment with Large Language Models
Venue: arXiv cs.CL 2024
Year: 2024

In recent years, large language models (LLMs) and generative AI have revolutionized natural language processing (NLP), offering unprecedented capabilities in education. This chapter explores the transformative potential of LLMs in automated question generation and answer assessment. It begins by examining the mechanisms behind LLMs, emphasizing their ability to comprehend and generate human-like text. The chapter then discusses methodologies for creating diverse, contextually relevant questions, enhancing learning through tailored, adaptive strategies. Key prompting techniques, such as zero-shot and chain-of-thought prompting, are evaluated for their effectiveness in generating high-quality questions, including open-ended and multiple-choice formats in various languages. Advanced NLP methods like fine-tuning and prompt-tuning are explored for their role in generating task-specific questions, despite associated costs. The chapter also covers the human evaluation of generated questions, highlighting quality variations across different methods and areas for improvement. Furthermore, it delves into automated answer assessment, demonstrating how LLMs can accurately evaluate responses, provide constructive feedback, and identify nuanced understanding or misconceptions. Examples illustrate both successful assessments and areas needing improvement. The discussion underscores the potential of LLMs to replace costly, time-consuming human assessments when appropriately guided, showcasing their advanced understanding and reasoning capabilities in streamlining educational processes.
A Game-Theoretic Perspective for Efficient Modern Random Access
Venue: arXiv cs.IT 2024
Year: 2024

Modern random access mechanisms combine packet repetitions with multi-user detection mechanisms at the receiver to maximize the throughput and reliability in massive Internet of Things (IoT) scenarios. However, optimizing the access policy, which selects the number of repetitions, is a complicated problem, and failing to do so can lead to an inefficient use of resources and, potentially, to an increased congestion. In this paper, we follow a game-theoretic approach for optimizing the access policies of selfish users in modern random access mechanisms. Our goal is to find adequate values for the rewards given after a success to achieve a Nash equilibrium (NE) that optimizes the throughput of the system while considering the cost of transmission. Our results show that a mixed strategy, where repetitions are selected according to the irregular repetition slotted ALOHA (IRSA) protocol, attains a NE that maximizes the throughput in the special case with two users. In this scenario, our method increases the throughput by 30% when compared to framed ALOHA. Furthermore, we present three methods to attain a NE with near-optimal throughput for general modern random access scenarios, which exceed the throughput of framed ALOHA by up to 34%.
FiRework: Field Refinement Framework for Efficient Enhancement of Deformable Registration
Venue: arXiv cs.CV 2024
Year: 2024

Deformable image registration remains a fundamental task in clinical practice, yet solving registration problems involving complex deformations remains challenging. Current deep learning-based registration methods employ continuous deformation to model large deformations, which often suffer from accumulated registration errors and interpolation inaccuracies. Moreover, achieving satisfactory results with these frameworks typically requires a large number of cascade stages, demanding substantial computational resources. Therefore, we propose a novel approach, the field refinement framework (FiRework), tailored for unsupervised deformable registration, aiming to address these challenges. In FiRework, we redesign the continuous deformation framework to mitigate the aforementioned errors. Notably, our FiRework requires only one level of recursion during training and supports continuous inference, offering improved efficacy compared to continuous deformation frameworks. We conducted experiments on two brain MRI datasets, enhancing two existing deformable registration networks with FiRework. The experimental results demonstrate the superior performance of our proposed framework in deformable registration. The code is publicly available at https://github.com/ZAX130/FiRework.
EmbodiedCity: A Benchmark Platform for Embodied Agent in Real-world City Environment
Venue: arXiv cs.AI 2024
Year: 2024

Embodied artificial intelligence emphasizes the role of an agent's body in generating human-like behaviors. The recent efforts on EmbodiedAI pay a lot of attention to building up machine learning models to possess perceiving, planning, and acting abilities, thereby enabling real-time interaction with the world. However, most works focus on bounded indoor environments, such as navigation in a room or manipulating a device, with limited exploration of embodying the agents in open-world scenarios. That is, embodied intelligence in the open and outdoor environment is less explored, for which one potential reason is the lack of high-quality simulators, benchmarks, and datasets. To address it, in this paper, we construct a benchmark platform for embodied intelligence evaluation in real-world city environments. Specifically, we first construct a highly realistic 3D simulation environment based on the real buildings, roads, and other elements in a real city. In this environment, we combine historically collected data and simulation algorithms to conduct simulations of pedestrian and vehicle flows with high fidelity. Further, we designed a set of evaluation tasks covering different EmbodiedAI abilities. Moreover, we provide a complete set of input and output interfaces for access, enabling embodied agents to easily take task requirements and current environmental observations as input and then make decisions and obtain performance evaluations. On the one hand, it expands the capability of existing embodied intelligence to higher levels. On the other hand, it has a higher practical value in the real world and can support more potential applications for artificial general intelligence. Based on this platform, we evaluate some popular large language models for embodied intelligence capabilities of different dimensions and difficulties.
Traversing Emotional Landscapes and Linguistic Patterns in Bernard-Marie Koltès' Plays: An NLP Perspective
Venue: arXiv cs.CL 2024
Year: 2024

This study employs Natural Language Processing (NLP) to analyze the intricate linguistic and emotional dimensions within the plays of Bernard-Marie Koltès, a central figure in contemporary French theatre. By integrating advanced computational techniques, we dissect Koltès' narrative style, revealing the subtle interplay between language and emotion across his dramatic oeuvre. Our findings highlight how Koltès crafts his narratives, enriching our understanding of his thematic explorations and contributing to the broader field of digital humanities in literary analysis.
Enhanced Electronic Health Records Text Summarization Using Large Language Models
Venue: arXiv cs.CL 2024
Year: 2024

The development of Electronic Health Records summarization systems has revolutionized patient data management. Previous research advanced this field by adapting Large Language Models for clinical tasks, using diverse datasets to generate general EHR summaries. However, clinicians often require specific, focused summaries for quicker insights. This project builds on prior work by creating a system that generates clinician-preferred, focused summaries, improving EHR summarization for more efficient patient care. The proposed system leverages the Google Flan-T5 model to generate tailored EHR summaries based on clinician-specified topics. The approach involved fine-tuning the Flan-T5 model on an EHR question-answering dataset formatted in the Stanford Question Answering Dataset (SQuAD) style, which is a large-scale reading comprehension dataset with questions and answers. Fine-tuning utilized the Seq2SeqTrainer from the Hugging Face Transformers library with optimized hyperparameters. Key evaluation metrics demonstrated promising results: the system achieved an Exact Match (EM) score of 81.81%. ROUGE (Recall-Oriented Understudy for Gisting Evaluation) metrics showed strong performance, with ROUGE-1 at 96.03%, ROUGE-2 at 86.67%, and ROUGE-L at 96.10%. Additionally, the Bilingual Evaluation Understudy (BLEU) score was 63%, reflecting the model's coherence in generating summaries. By enhancing EHR summarization through LLMs, this project supports digital transformation efforts in healthcare, streamlining workflows, and enabling more personalized patient care.
SciGisPy: a Novel Metric for Biomedical Text Simplification via Gist Inference Score
Venue: arXiv cs.CL 2024
Year: 2024

Biomedical literature is often written in highly specialized language, posing significant comprehension challenges for non-experts. Automatic text simplification (ATS) offers a solution by making such texts more accessible while preserving critical information. However, evaluating ATS for biomedical texts is still challenging due to the limitations of existing evaluation metrics. General-domain metrics like SARI, BLEU, and ROUGE focus on surface-level text features, and readability metrics like FKGL and ARI fail to account for domain-specific terminology or assess how well the simplified text conveys core meanings (gist). To address this, we introduce SciGisPy, a novel evaluation metric inspired by Gist Inference Score (GIS) from Fuzzy-Trace Theory (FTT). SciGisPy measures how well a simplified text facilitates the formation of abstract inferences (gist) necessary for comprehension, especially in the biomedical domain. We revise GIS for this purpose by introducing domain-specific enhancements, including semantic chunking, Information Content (IC) theory, and specialized embeddings, while removing unsuitable indexes. Our experimental evaluation on the Cochrane biomedical text simplification dataset demonstrates that SciGisPy outperforms the original GIS formulation, with a significant increase in correctly identified simplified texts (84% versus 44.8%). The results and a thorough ablation study confirm that SciGisPy better captures the essential meaning of biomedical content, outperforming existing approaches.
Reducing Data Bottlenecks in Distributed, Heterogeneous Neural Networks
Venue: arXiv cs.DC 2024
Year: 2024

The rapid advancement of embedded multicore and many-core systems has revolutionized computing, enabling the development of high-performance, energy-efficient solutions for a wide range of applications. As models scale up in size, data movement is increasingly the bottleneck to performance. This movement of data can exist between processor and memory, or between cores and chips. This paper investigates the impact of bottleneck size, in terms of inter-chip data traffic, on the performance of deep learning models in embedded multicore and many-core systems. We conduct a systematic analysis of the relationship between bottleneck size, computational resource utilization, and model accuracy. We apply a hardware-software co-design methodology where data bottlenecks are replaced with extremely narrow layers to reduce the amount of data traffic. In effect, time-multiplexing of signals is replaced by learnable embeddings that reduce the demands on chip IOs. Our experiments on the CIFAR100 dataset demonstrate that the classification accuracy generally decreases as the bottleneck ratio increases, with shallower models experiencing a more significant drop compared to deeper models. Hardware-side evaluation reveals that higher bottleneck ratios lead to substantial reductions in data transfer volume across the layers of the neural network. Through this research, we can determine the trade-off between data transfer volume and model performance, enabling the identification of a balanced point that achieves good performance while minimizing data transfer volume. This characteristic allows for the development of efficient models that are well-suited for resource-constrained environments.
ALLoRA: Adaptive Learning Rate Mitigates LoRA Fatal Flaws
Venue: arXiv cs.LG 2024
Year: 2024

Low-Rank Adaptation (LoRA) is the bread and butter of Large Language Model (LLM) finetuning. LoRA learns an additive low-rank perturbation, $AB$, of a pretrained matrix parameter $W$ to align the model to a new task or dataset with $W+AB$. We identify three core limitations to LoRA for finetuning--a setting that employs limited amount of data and training steps. First, LoRA employs Dropout to prevent overfitting. We prove that Dropout is only suitable for long training episodes but fails to converge to a reliable regularizer for short training episodes. Second, LoRA's initialization of $B$ at $0$ creates a slow training dynamic between $A$ and $B$. That dynamic is also exacerbated by Dropout that further slows the escape from $0$ for $B$ which is particularly harmful for short training episodes. Third, the scaling factor multiplying each LoRA additive perturbation creates ``short-sighted'' interactions between the LoRA modules of different layers. Motivated by principled analysis of those limitations, we find an elegant solution: a Dropout-free, scaling-free, LoRA with Adaptive Learning rate--coined ALLoRA. By scaling the per sample and per parameter gradients with a coefficient inversely proportional to parameters' $\ell_2$ norm, ALLoRA alleviates those three limitations. As a by-product, ALLoRA removes two hyper-parameters from LoRA: the scaling factor and the dropout rate. Empirical results show that ALLoRA admits better accuracy than LoRA on various settings, including against recent LoRA variants such as Weight-Decomposed Low-Rank Adaptation (DoRA). Ablation studies show our solution is the optimal in a family of weight-dependent / output-dependent approaches on various LLMs including the latest Llama3.
Scalable Weibull Graph Attention Autoencoder for Modeling Document Networks
Venue: arXiv cs.LG 2024
Year: 2024

Although existing variational graph autoencoders (VGAEs) have been widely used for modeling and generating graph-structured data, most of them are still not flexible enough to approximate the sparse and skewed latent node representations, especially those of document relational networks (DRNs) with discrete observations. To analyze a collection of interconnected documents, a typical branch of Bayesian models, specifically relational topic models (RTMs), has proven their efficacy in describing both link structures and document contents of DRNs, which motives us to incorporate RTMs with existing VGAEs to alleviate their potential issues when modeling the generation of DRNs. In this paper, moving beyond the sophisticated approximate assumptions of traditional RTMs, we develop a graph Poisson factor analysis (GPFA), which provides analytic conditional posteriors to improve the inference accuracy, and extend GPFA to a multi-stochastic-layer version named graph Poisson gamma belief network (GPGBN) to capture the hierarchical document relationships at multiple semantic levels. Then, taking GPGBN as the decoder, we combine it with various Weibull-based graph inference networks, resulting in two variants of Weibull graph auto-encoder (WGAE), equipped with model inference algorithms. Experimental results demonstrate that our models can extract high-quality hierarchical latent document representations and achieve promising performance on various graph analytic tasks.
Honest AI: Fine-Tuning "Small" Language Models to Say "I Don't Know", and Reducing Hallucination in RAG
Venue: arXiv cs.CL 2024
Year: 2024

Hallucination is a key roadblock for applications of Large Language Models (LLMs), particularly for enterprise applications that are sensitive to information accuracy. To address this issue, two general approaches have been explored: Retrieval-Augmented Generation (RAG) to supply LLMs with updated information as context, and fine-tuning the LLMs with new information and desired output styles. In this paper, we propose Honest AI: a novel strategy to fine-tune "small" language models to say "I don't know" to reduce hallucination, along with several alternative RAG approaches. The solution ranked 1st in Task 2 for the false premise question. The alternative approaches include using RAG with search engine and knowledge graph results, fine-tuning base LLMs with new information and combinations of both approaches. Although all approaches improve the performance of the LLMs, RAG alone does not significantly improve the performance and fine-tuning is needed for better results. Finally, the hybrid approach achieved the highest score in the CRAG benchmark. In addition, our approach emphasizes the use of relatively small models with fewer than 10 billion parameters, promoting resource efficiency.
Flying Quadrotors in Tight Formations using Learning-based Model Predictive Control
Venue: arXiv cs.RO 2024
Year: 2024

Flying quadrotors in tight formations is a challenging problem. It is known that in the near-field airflow of a quadrotor, the aerodynamic effects induced by the propellers are complex and difficult to characterize. Although machine learning tools can potentially be used to derive models that capture these effects, these data-driven approaches can be sample inefficient and the resulting models often do not generalize as well as their first-principles counterparts. In this work, we propose a framework that combines the benefits of first-principles modeling and data-driven approaches to construct an accurate and sample efficient representation of the complex aerodynamic effects resulting from quadrotors flying in formation. The data-driven component within our model is lightweight, making it amenable for optimization-based control design. Through simulations and physical experiments, we show that incorporating the model into a novel learning-based nonlinear model predictive control (MPC) framework results in substantial performance improvements in terms of trajectory tracking and disturbance rejection. In particular, our framework significantly outperforms nominal MPC in physical experiments, achieving a 40.1% improvement in the average trajectory tracking errors and a 57.5% reduction in the maximum vertical separation errors. Our framework also achieves exceptional sample efficiency, using only a total of 46 seconds of flight data for training across both simulations and physical experiments. Furthermore, with our proposed framework, the quadrotors achieve an exceptionally tight formation, flying with an average separation of less than 1.5 body lengths throughout the flight. A video illustrating our framework and physical experiments is given here: https://youtu.be/Hv-0JiVoJGo
'Quis custodiet ipsos custodes?' Who will watch the watchmen? On Detecting AI-generated peer-reviews
Venue: arXiv cs.CL 2024
Year: 2024

The integrity of the peer-review process is vital for maintaining scientific rigor and trust within the academic community. With the steady increase in the usage of large language models (LLMs) like ChatGPT in academic writing, there is a growing concern that AI-generated texts could compromise scientific publishing, including peer-reviews. Previous works have focused on generic AI-generated text detection or have presented an approach for estimating the fraction of peer-reviews that can be AI-generated. Our focus here is to solve a real-world problem by assisting the editor or chair in determining whether a review is written by ChatGPT or not. To address this, we introduce the Term Frequency (TF) model, which posits that AI often repeats tokens, and the Review Regeneration (RR) model, which is based on the idea that ChatGPT generates similar outputs upon re-prompting. We stress test these detectors against token attack and paraphrasing. Finally, we propose an effective defensive strategy to reduce the effect of paraphrasing on our models. Our findings suggest both our proposed methods perform better than the other AI text detectors. Our RR model is more robust, although our TF model performs better than the RR model without any attacks. We make our code, dataset, and model public.
Look-and-Twist: A Simple Selection Method for Virtual and Augmented Reality
Venue: arXiv cs.HC 2024
Year: 2024

This paper introduces a novel interaction method for virtual and augmented reality called look-and-twist, which is directly analogous to point-and-click operations using a mouse and desktop. It is based on head rotation alone and is straightforward to implement on any head mounted display that performs rotational tracking. A user selects features of interest by turning their head to face an object, and then performs a specified rotation along the axis of the looking direction. The look-and-twist method has been implemented and tested in an educational context, and systematic user studies are underway. Early evidence indicates that the method is comparable to, or faster than, the standard dwell time method. The method can be used, for example, with Google Cardboard, and it is straightforward to learn for inexperienced users. Moreover, it has the potential to significantly enrich VR interactions by providing an additional degree of freedom of control, which the binary nature of dwell-based methods lacks.